k.test {KODAMA} | R Documentation |
This function performs a permutation test using PLS to assess association between the KODAMA output and any additional related parameters such as clinical metadata.
k.test(data, labels, n = 100)
data |
a matrix. |
labels |
a classification vector. |
n |
number of iterations of the permutation test. |
The p-value of the test.
Stefano Cacciatore
Cacciatore S, Luchinat C, Tenori L
Knowledge discovery by accuracy maximization.
Proc Natl Acad Sci U S A 2014;111(14):5117-22. doi: 10.1073/pnas.1220873111. Link
Cacciatore S, Tenori L, Luchinat C, Bennett PR, MacIntyre DA
KODAMA: an updated R package for knowledge discovery and data mining.
Bioinformatics 2017;33(4):621-623. doi: 10.1093/bioinformatics/btw705. Link
# data(iris) # data=iris[,-5] # labels=iris[,5] # kk=KODAMA(data,FUN="PLS-DA") # kkplot=kk$pp # k1=k.test(kkplot,labels) # print(k1) # k2=k.test(kkplot,sample(labels)) # print(k2)